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Backbone model based on cryo-EM MAP at 8.5 a of domain-swapped, glycan-reactive, neutralizing antibody 2G12 bound to HIV-1 env BG505 ds-sosip, which was also bound to CD4-binding site antibody VRC03

Analyse Backbone model based on cryo-EM MAP at 8.5 a of domain-swapped… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6E5P
Type: protein
Length: 5,046 residues
Chains: 24
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 2G12 light chain; 2G12 heavy chain; Envelope glycoprotein GP120; Envelope glycoprotein…
UniProt: Q2N0S6, Q2N0S9
Ligands: MAN, NAG, BMA
Pockets: 20 · best druggability 0.74

Structure

electron microscopy · 6 distinct chains · 13% helix, 38% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
1, 4, K, L, Q, T	2G12 light chain	protein	212	5% helix, 35% strand	—
2, 3, H, M, R, S	2G12 heavy chain	protein	225	8% helix, 44% strand	—
A, C, E	Envelope glycoprotein GP120	protein	453	14% helix, 39% strand	Q2N0S6
B, D, F	Envelope glycoprotein GP160	protein	126	52% helix, 6% strand	Q2N0S9
I, O, V	VRC03 heavy chain	protein	128	7% helix, 50% strand	—
J, P, W	VRC03 light chain	protein	101	3% helix, 50% strand	—

Ligands and binding sites

MAN · alpha-D-mannopyranose · sugar · 54 copies · chains 2, 1, 3, 4, H, M, S, R, L, K, Q, T
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 24 copies · chains E, A, C
BMA · beta-D-mannopyranose · sugar · 12 copies

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	947	0.74	0.79	74	empty
2	924	0.74	0.79	77	empty
3	943	0.74	0.79	78	empty
4	917	0.74	0.79	76	empty
5	933	0.74	0.78	76	empty

Interfaces

42 interfaces between chains.

A–B · 621 Å² buried · 6 hydrogen bonds · protein-protein
E–F · 620 Å² buried · 6 hydrogen bonds · protein-protein
C–D · 619 Å² buried · 6 hydrogen bonds · protein-protein
K–M · 215 Å² buried · 0 hydrogen bonds · protein-protein
Q–R · 215 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

6E5P · Backbone model based on cryo-EM map at 8.5 A of domain-swapped, glycan-reactive… · the same entry in another collection · chain 1 against 1, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q2N0S6
Every structure of UniProt Q2N0S9
Elsewhere: RCSB PDB 6E5P · PDBe 6E5P · UniProt Q2N0S6 · UniProt Q2N0S9

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